BioC 3.5: CHECK report for mgsa on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings mgsa_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/mgsa.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mgsa/DESCRIPTION’ ... OK
* this is package ‘mgsa’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mgsa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘mgsa’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘gplots’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘DBI’ ‘GO.db’ ‘RSQLite’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘gplots’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createMgsaGoSets: no visible global function definition for ‘new’
mcmcSummary: no visible binding for global variable ‘sd’
mgsa.wrapper: no visible global function definition for ‘str’
mgsa.wrapper: no visible global function definition for ‘new’
readGAF: no visible global function definition for ‘read.delim’
readGAF: no visible global function definition for ‘na.omit’
readGAF: no visible global function definition for ‘new’
initialize,MgsaSets: no visible global function definition for
  ‘callNextMethod’
initialize,MgsaSets: no visible global function definition for ‘relist’
mgsa,character-MgsaSets: no visible global function definition for
  ‘na.omit’
plot,MgsaResults: no visible global function definition for
  ‘split.screen’
plot,MgsaResults: no visible global function definition for ‘screen’
plot,MgsaResults: no visible global function definition for ‘par’
plot,MgsaResults: no visible global function definition for ‘barplot2’
plot,MgsaResults: no visible global function definition for
  ‘close.screen’
Undefined global functions or variables:
  barplot2 callNextMethod close.screen na.omit new par read.delim
  relist screen sd split.screen str
Consider adding
  importFrom("graphics", "close.screen", "par", "screen", "split.screen")
  importFrom("methods", "callNextMethod", "new")
  importFrom("stats", "na.omit", "sd")
  importFrom("utils", "read.delim", "relist", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
  src/Makevars.in
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
         user system elapsed
readGAF 5.104  0.192   6.359
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/mgsa.Rcheck/00check.log’
for details.

* installing *source* package ‘mgsa’ ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c mgsa-core.c -o mgsa-core.o
mgsa-core.c:796:13: warning: ‘print_context’ defined but not used [-Wunused-function]
 static void print_context(struct context *cn)
             ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c mgsa.c -o mgsa.o
mgsa.c: In function ‘create_parameter_prior_from_R’:
mgsa.c:52:10: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  if (!(p = R_alloc(1,sizeof(*p))))
          ^
mgsa.c:65:19: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   if (!(p->values = R_alloc(p->number_of_states,sizeof(p->values[0]))))
                   ^
mgsa.c: In function ‘create_summary_for_param_from_R’:
mgsa.c:177:19: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   if (!(sum->dmap = R_alloc(number_of_discrete_values,sizeof(sum->dmap[0]))))
                   ^
mgsa.c: In function ‘mgsa_mcmc’:
mgsa.c:407:7: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   nas = R_alloc(las,sizeof(nas[0]));
       ^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c mt.c -o mt.o
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o mgsa.so mgsa-core.o mgsa.o mt.o -fopenmp -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/mgsa.Rcheck/mgsa/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mgsa)

name	user	system	elapsed
MgsaSets-class	0.06	0.00	0.06
mgsa-methods	2.008	0.020	1.737
readGAF	5.104	0.192	6.359

BioC 3.5: CHECK report for mgsa on malbec2

Summary

Command output